[CP2K:4532] Re: Comparing the energy from cp2k and gromacs

[Peter Mamonov]

Hello Fahimeh,

Check the energy components: bonds, angles, torsion angles, coulomb and
vdw. I believe the bonded interactions energies should agree perfectly,
otherwise there is a mismatch between topologies and/or forcefield you use
in gromacs and cp2k. If those are ok, then I guess this discrepancy is due
to differences in PME electrostatics calculation/implementation.

Regards,
Peter


On Tue, Aug 6, 2013 at 8:00 PM, Fahimeh Baftizadeh <
fahimeh.b... at googlemail.com> wrote:

> Hello everyone,
>
> I thought maybe it will be helpful if I just put here my input files and
> someone else run it if it is possible for you. In fact it seems very
> trivial but I checked the parameters and I don't understand why the Energy
> is positive!
>
> I am doing just a single step energy calculation of a molecule.
> Thanks for your help
>
> Fahimeh
>
>
>
> On Monday, August 5, 2013 4:53:08 PM UTC-4, Fahimeh Baftizadeh wrote:
>>
>> Hello,
>>
>> I have a system which contains only one molecule in gas phase. I wanna
>> compute its energy with cp2k and gromacs (for a test).
>> I am reading a pdb file and the force filed is in amber format, this is
>> cp2k input file:
>>
>> &FORCE_EVAL
>>   METHOD FIST
>>   &MM
>>     &FORCEFIELD
>>       &SPLINE
>>         EMAX_ACCURACY 500.0
>>         EMAX_SPLINE    1000.0
>>         EPS_SPLINE [hartree] 1.00000000E-07
>>       &END
>>       parm_file_name /home/fbafti/work/nucleation/**
>> test-ff/single-mol/amber-1res.**top
>>       parmtype AMBER
>>     &END FORCEFIELD
>>     &POISSON
>>      &EWALD
>>        EWALD_TYPE pme
>>        RCUT [angstrom] 8.0
>>        EPSILON 1E-6
>>      &END EWALD
>>     &END POISSON
>>     &PRINT
>>       &FF_INFO
>>       &END
>>     &END
>>   &END MM
>>   &SUBSYS
>>     &CELL
>>       ABC 125.990  122.910  129.640
>>     &END
>>     &TOPOLOGY
>>      COORD_FILE_NAME /home/fbafti/work/nucleation/**
>> test-ff/single-mol/non-per.pdb
>>      COORDINATE PDB
>>      CONN_FILE_NAME  /home/fbafti/work/nucleation/**
>> test-ff/single-mol/amber-1res.**top
>>      CONN_FILE_FORMAT  AMBER
>>     &END TOPOLOGY
>>   &END SUBSYS
>>   STRESS_TENSOR ANALYTICAL
>> &END FORCE_EVAL
>> &GLOBAL
>>   PROJECT paracetamol_single_mol
>>   RUN_TYPE ENERGY
>> &END GLOBAL
>>
>>
>> I put a very large box size, just to be sure that there are no periodic
>> images in the energy estimation. The energy output of CP2K has a value
>> which is larger than zero and it is strange.
>> I performed a single step steepest decent with gromacs and I got another
>> value which is minus and makes more sense.
>> I already checked the electrostatic parameters and vdw ... I think they
>> are all similar while the energy difference coming from gromacs and
>> cp2k differs by almost 500 kj/mol and in gromacs is minus and in cp2k is a
>> plus value.
>>
>> This is the gromacs input file:
>>
>> integrator               = steep
>> comm_mode                = Linear
>> dt                       = 0.001
>> nsteps                   = 1
>> ; Output frequency for coords (x), velocities (v) and forces (f) =
>> nstxout                  = 1
>> nstvout                  = 1
>> ; Output frequency for energies to log file and energy file =
>> nstlog                   = 1
>> nstenergy                = 1
>> nstxtcout                = 1
>> xtc-precision            = 1000000
>> xtc_grps                 = System
>> energygrps               = System
>> pbc                      = xyz
>> nstlist                  = 10
>> epsilon_r                = 1.
>> ns_type                  = grid ; or grid I don't know
>> coulombtype              = pme
>> vdwtype                  = Cut-off
>> fourierspacing           = 0.12
>> ; EWALD/PME/PPPM parameters
>> pme_order                = 4
>> ewald_rtol               = 1e-05
>> epsilon_surface          = 0
>> optimize_fft             = yes
>> rlist                    = 0.8
>> rcoulomb                 = 0.8
>> rvdw                     = 0.8
>> emtol                    = 1.0
>>
>> Can anybody help me with that?
>> Thanks
>> Fahimeh
>>
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